Due to the rapid expansion of tourism, mining, and manufacturing, the economy of Hainan Island in southern China has experienced swift growth. However, it also brings the risk of soil pollution by mercury (Hg) as a result of increased traffic and mineral processing activities. In order to investigate the characteristics of soil Hg pollution in Hainan Island and assess the health risk, a total of 239 samples were gathered from five representative regions across the island. The findings indicate considerable fluctuations in the soil Hg concentration across the five sub-study areas, which are influenced by factors such as wind direction, mining activities, and economic development. Changjiang Li Autonomous County, situated in the downwind direction (NW) and rich in mineral resources, shows the highest soil Hg concentration (10.00–1582.50 ng·g−1). Following closely are Haikou and Sanya, the two most economically developed cities on the island, with soil Hg concentrations of 8.33–321.50 ng·g−1 and 6.04–180.50 ng·g−1, respectively. Wuzhishan Nature Reserve and Lingshui Li Autonomous County, located in the upwind area (SE), show the lowest concentrations, ranging between 10.70–104.67 ng·g−1 and 9.43–84.00 ng·g−1, respectively. Both the Single Pollution Index method and the Geo-accumulation Index method were employed to assess the level of Hg pollution. The results indicate that nearly half of the sampling sites are contaminated, in which the proportion of contaminated sites in Sanya and Haikou are the highest, but the level of contamination is low; the heavily contaminated sites are predominantly found in Changjiang Li Autonomous County. However, the low Health Risk Index (HI) ranging from 0.0001 to 0.0334 suggests that although the soil is contaminated with Hg, it does not pose a substantial non-carcinogenic risk to human health.